From a5dc2bc87a7fc83b3ca8e3bda4a96bf3256191e6 Mon Sep 17 00:00:00 2001
From: payno <payno@linazimov.esrf.fr>
Date: Mon, 30 Sep 2019 08:49:05 +0200
Subject: [PATCH] [h5py] add opening mode in h5py.File
---
est/core/process/pymca/test/test_io.py | 2 +-
est/core/process/pymca/test/test_normalization.py | 2 +-
est/core/process/pymca/test/test_workflow.py | 2 +-
est/core/process/test/test_roi.py | 2 +-
est/core/test/test_types.py | 2 +-
est/core/types.py | 6 +++---
est/io/io.py | 6 +++---
orangecontrib/est/test/test_larch_workflow.py | 2 +-
8 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/est/core/process/pymca/test/test_io.py b/est/core/process/pymca/test/test_io.py
index 7e20beb3..da3cf2bc 100644
--- a/est/core/process/pymca/test/test_io.py
+++ b/est/core/process/pymca/test/test_io.py
@@ -84,7 +84,7 @@ class TestNxWriting(unittest.TestCase):
writer = XASWriter()
writer.output_file = self.h5_file
writer(self.xas_obj)
- with h5py.File(self.h5_file) as hdf:
+ with h5py.File(self.h5_file, 'r') as hdf:
self.assertTrue('scan1' in hdf.keys())
self.assertTrue('data' in hdf['scan1'].keys())
self.assertTrue('absorbed_beam' in hdf['scan1'].keys())
diff --git a/est/core/process/pymca/test/test_normalization.py b/est/core/process/pymca/test/test_normalization.py
index 7f7aca36..df883b08 100644
--- a/est/core/process/pymca/test/test_normalization.py
+++ b/est/core/process/pymca/test/test_normalization.py
@@ -85,7 +85,7 @@ class TestNormalizationMultipleSpectrum(unittest.TestCase):
spectra_path = '/data/NXdata/data'
channel_path = '/data/NXdata/Channel'
filename = os.path.join(self.output_dir, 'myfile.h5')
- with h5py.File(filename) as f:
+ with h5py.File(filename, 'w') as f:
f[spectra_path] = self.spectra
f[channel_path] = self.energy
diff --git a/est/core/process/pymca/test/test_workflow.py b/est/core/process/pymca/test/test_workflow.py
index 54beb64e..5ede0493 100644
--- a/est/core/process/pymca/test/test_workflow.py
+++ b/est/core/process/pymca/test/test_workflow.py
@@ -245,7 +245,7 @@ class TestSaveFlowAuto(unittest.TestCase):
writer.output_file = self.h5_file
writer(out)
- with h5py.File(self.h5_file) as hdf:
+ with h5py.File(self.h5_file, 'r') as hdf:
self.assertTrue('scan1' in hdf.keys())
self.assertTrue('data' in hdf['scan1'].keys())
self.assertTrue('absorbed_beam' in hdf['scan1'].keys())
diff --git a/est/core/process/test/test_roi.py b/est/core/process/test/test_roi.py
index d7e64071..8c320278 100644
--- a/est/core/process/test/test_roi.py
+++ b/est/core/process/test/test_roi.py
@@ -49,7 +49,7 @@ class TestRoi(unittest.TestCase):
spectra_path = '/data/NXdata/data'
channel_path = '/data/NXdata/Channel'
filename = os.path.join(self.output_dir, 'myfile.h5')
- with h5py.File(filename) as f:
+ with h5py.File(filename, 'w') as f:
f[spectra_path] = self.spectra
f[channel_path] = self.energy
diff --git a/est/core/test/test_types.py b/est/core/test/test_types.py
index 3495d185..2d3892cb 100644
--- a/est/core/test/test_types.py
+++ b/est/core/test/test_types.py
@@ -100,7 +100,7 @@ class TestXASObject(unittest.TestCase):
spectra_path = '/data/NXdata/data'
channel_path = '/data/NXdata/Channel'
filename = os.path.join(self.output_dir, 'myfile.h5')
- with h5py.File(filename) as f:
+ with h5py.File(filename, 'w') as f:
f[spectra_path] = self.spectra
f[channel_path] = self.energy
diff --git a/est/core/types.py b/est/core/types.py
index dc677dac..9cf27427 100644
--- a/est/core/types.py
+++ b/est/core/types.py
@@ -489,7 +489,7 @@ class XASObject(object):
'stored')
else:
process_flow = self.get_process_flow()
- with h5py.File(self.linked_h5_file) as h5f:
+ with h5py.File(self.linked_h5_file, 'w') as h5f:
for index, process_ in process_flow.items():
del h5f[process_['_h5py_path']]
@@ -505,8 +505,8 @@ class XASObject(object):
flow = self.get_process_flow()
entry = self.entry
- with h5py.File(self.__h5_file) as source_hdf:
- with h5py.File(h5_file_target) as target_hdf:
+ with h5py.File(self.__h5_file, 'w') as source_hdf:
+ with h5py.File(h5_file_target, 'w') as target_hdf:
target_entry = target_hdf.require_group(entry)
def remove_entry_prefix(name):
return name.replace('/'+entry+'/', '', 1)
diff --git a/est/io/io.py b/est/io/io.py
index be6ec249..e7300c6a 100644
--- a/est/io/io.py
+++ b/est/io/io.py
@@ -148,7 +148,7 @@ def write_xas_proc(h5_file, entry, process, data, processing_order,
"""
process_name = 'xas_process_' + str(processing_order)
# write the xasproc
- with h5py.File(h5_file) as h5f:
+ with h5py.File(h5_file, 'w') as h5f:
nx_entry = h5f.require_group('/'.join((data_path, entry)))
nx_entry.attrs["NX_class"] = "NXentry"
@@ -216,7 +216,7 @@ def write_xas(h5_file, entry, energy, mu, sample=None, start_time=None,
:param str title: experiment title
:param str definition: experiment definition
"""
- with h5py.File(h5_file) as h5f:
+ with h5py.File(h5_file, 'w') as h5f:
nx_entry = h5f.require_group('/'.join((data_path, entry)))
nx_entry.attrs["NX_class"] = "NXentry"
@@ -297,7 +297,7 @@ def get_xasproc(h5_file, entry):
return res
res = []
- with h5py.File(h5_file) as h5f:
+ with h5py.File(h5_file, 'w') as h5f:
try:
root_group = h5f[entry]
except KeyError:
diff --git a/orangecontrib/est/test/test_larch_workflow.py b/orangecontrib/est/test/test_larch_workflow.py
index cbe5119d..779dbc38 100644
--- a/orangecontrib/est/test/test_larch_workflow.py
+++ b/orangecontrib/est/test/test_larch_workflow.py
@@ -132,7 +132,7 @@ class TestSimpleLarchWorkflow(OrangeWorflowTest):
self.assertTrue(os.path.exists(self.output_file))
# test outputfile
- with h5py.File(self.output_file) as hdf5:
+ with h5py.File(self.output_file, 'r') as hdf5:
self.assertTrue('scan1' in hdf5)
scan_grp = hdf5['scan1']
self.assertTrue('absorbed_beam' in scan_grp)
--
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